Recent flight experiments on the Space Shuttle Orbiter during re-entry have provided striking visual evidence of boundary layer transition, as well as a wealth of new quantitative data for stability and transition analysis. In this paper, we make a first attempt to analyze a portion of the data taken during the Boundary Layer Transition Flight Experiment and the Hypersonic Thermodynamic Infrared Measurement campaign for STS-119. We use the mean flow data for the Shuttle Orbiter obtained in a companion paper on a high-resolution grid of the Orbiter windward surface. New data extraction and boundary layer analysis tools are used to study the boundary layer properties, as well as to compare with the discrete thermocouple data and the infrared imagery from the flight experiments. For the limited number of cases studied, we find that two standard approaches for correlating boundary layer transition, Reθ/Me and Rek, are incomplete measures of boundary layer stability for the full windside surface. Furthermore, the momentum thickness θ and edge Mach number Me are nearly constant for much of the Orbiter windside for the trajectory points considered here. Thus, (as Reshotko has argued) the Reθ/Me parameter is simply a surrogate for the free-stream density. Having made this observation, this parameter appears to be more relevant for characterizing boundary layer stability on the Orbiter centerline than the roughness Reynolds number. This message is the opposite on the wings, with Rek being the more relevant stability metric. We are working towards a fully threedimensional stability analysis tool for these flows to provide a mechanism-based argument for these observations.